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- PDB-9ech: PANK3 complex structure with compound PZ-5578 -

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Basic information

Entry
Database: PDB / ID: 9ech
TitlePANK3 complex structure with compound PZ-5578
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator
Function / homology
Function and homology information


Coenzyme A biosynthesis / acetyl-CoA binding / vitamin binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
: / ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.043 Å
AuthorsYun, M. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Isoform Selectivity Driven Pantothenate Kinases Activation by Novel Sulfonamide Analogues of Pantazines
Authors: Tangallapally, R. / Coker, A. / Edwards, A. / Subramanian, C. / Jayasinghe, T. / Yun, M. / Jackowski, S. / Rock, C.O. / White, S.W. / Lee, R.E.
History
DepositionNov 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2637
Polymers42,1261
Non-polymers1,1386
Water1,29772
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,52714
Polymers84,2522
Non-polymers2,27512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area10560 Å2
ΔGint-39 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.374, 98.374, 68.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pantothenate kinase 3 / hPanK3 / Pantothenic acid kinase 3


Mass: 42125.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H999, pantothenate kinase

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Non-polymers , 6 types, 78 molecules

#2: Chemical ChemComp-A1BHH / N-(3-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)ethanesulfonamide


Mass: 423.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22ClN5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.043→32.2 Å / Num. obs: 24713 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 43.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.8
Reflection shellResolution: 2.043→2.078 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1212 / CC1/2: 0.35 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.043→32.2 Å / SU ML: 0.2912 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.5802 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227 1206 4.88 %
Rwork0.2061 23494 -
obs0.207 24700 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.32 Å2
Refinement stepCycle: LAST / Resolution: 2.043→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 0 72 72 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182831
X-RAY DIFFRACTIONf_angle_d0.47563831
X-RAY DIFFRACTIONf_chiral_restr0.0381422
X-RAY DIFFRACTIONf_plane_restr0.0028483
X-RAY DIFFRACTIONf_dihedral_angle_d9.49071639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.043-2.120.33551460.32662529X-RAY DIFFRACTION99.74
2.12-2.220.33441360.29552597X-RAY DIFFRACTION99.93
2.22-2.340.32661360.272571X-RAY DIFFRACTION100
2.34-2.480.27051440.25092568X-RAY DIFFRACTION99.96
2.48-2.680.25211360.22212601X-RAY DIFFRACTION100
2.68-2.950.22831440.20732587X-RAY DIFFRACTION100
2.95-3.370.2179930.19812656X-RAY DIFFRACTION100
3.37-4.250.17951070.18192671X-RAY DIFFRACTION99.96
4.25-32.20.21181640.1892714X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 29.8940376073 Å / Origin y: 8.00030498907 Å / Origin z: 4.98223247427 Å
111213212223313233
T0.347356834254 Å20.0262000725876 Å20.0040609415438 Å2-0.267215760162 Å2-3.63443424146E-5 Å2--0.266157399467 Å2
L1.60198549269 °20.477842581976 °20.565764943358 °2-3.1684735717 °21.44053894674 °2--2.21329961586 °2
S0.00641781592774 Å °-0.129262254695 Å °0.081448927322 Å °0.58261173934 Å °-0.0247668733404 Å °-0.0605320696054 Å °0.277551955745 Å °0.064149565577 Å °0.0166680035521 Å °
Refinement TLS groupSelection details: all

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